If there is a signed bill showing full payment, then it should generally help you. The general rule is that a document can be proved by its own contents. Oral statement about the contents of a document is secondary evidence, which may be inadmissible if the primary evidence (i.e., the document itself) is available.
From what you write, there appears to be defect in evidence against you. You may have to either challenge the action against you in appropriate court, or to prove your case in the departmental inquiry. However, since your question is a question of facts, someone has to examine the documents / evidence in details. Please consult some local lawyer at your place with your documents, who can then guide you after detailed examination of the papers.
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